Background: Although the effects of footwear type on joint stiffness have previously been investigated, researchers did not consider foot flexibility. Thus, the present investigation aimed to determine the interaction effects of footwear type, static navicular drop and dynamic ankle pronation on dynamic joint stiffness in running. Research question: Does the footwear types in interaction with the foot posture affect the stiffness of the joints of the lower limb? Methods: Forty-seven male individuals participated in this study. Firstly, they were divided into the high navicular, low navicular, and normal navicular drop. Secondly, they were divided into the high dynamic ankle pronation, low dynamic ankle pronation, and normal dynamic ankle pronation groups. Participants performed three running trials at 3 ± 0.2 m/s at minimalist footwear, conventional footwear, and barefoot conditions. We collected the ground reaction forces and three-dimensional kinematic data and calculated joint stiffness over the stance phase. Results: There was no significant main effect of navicular drop or dynamic ankle pronation on dynamic joint stiffness for the ankle, knee, and hip (p > 0.05). However, footwear type significantly affected dynamic joint stiffness. The pairwise comparison revealed that the ankle and hip dynamic joint stiffness magnitudes in the conventional footwear condition were greater than in the barefoot and minimalist footwear conditions (p 0.001). In contrast, the knee dynamic joint stiffness magnitude in the conventional footwear condition was lesser than in barefoot and minimalist footwear conditions (p 0.001). Significance: The navicular drop or dynamic ankle pronation did not influence lower limb joint stiffness, and there was no significant interaction between navicular drop or dynamic ankle pronation and footwear on lower limb dynamic joint stiffness. However, conventional footwear increased the ankle and hip dynamic joint stiffness while reducing knee dynamic joint stiffness, leading to changes in transfer energy, which could have implications for relative injury risk